Sphere Grid probably. On one hand the license Board was too open, it did allow you to make any class you want, but often that meant the character became a jack of all trades, plus I think it makes a better character if they are more inclined to a specific class. Requiring licenses to use armour was also a pain, same with having to buy gambits. Crystarium on the other hand was a bit too closed off, you were forced to pick up abilities which you probably didn't want, and the side classes required a stupid amount of CP to learn. The sphere grid gave a nice balance, the international/expert grid, anyway. There was a main path for that specific character and then it branched off into other characters paths, which you could go off onto, if you so please. My only problem is could be troublesome to get back to the place where it does branch off into a specific characters path.
Reason why I dislike the Job system always was that each Job had seperate levels, and you couldn't use other classes abilities in battle. Consequently, if you got quite late on in the game, and decided, I need to have someone as that job, well then you have to start back at level 1 in terms of your job, and then go grind for it, to get abilities for that job, the character your grinding for, often being useless in battle until they learn some worth while abilities. Where as with the more recent systems, you can get spheres/crystals/licenses for a different class(or atleast abilities that would be designated to that class, if there was a class) while battling in another class. Not to mention, with the job class, you don't really have the ability to use other classes ability in battle, unless you set yourself as that other class, unlike the later ones, where you can. Although admittedly in XIII, you still have to swap class, you are just able to in the middle of battle.
Oh, and by the way, for the most case in X(Once you start going down other characters paths, that does change, though, true), and all through XIII(Each of their Crystarium paths for classes are all unique, so although all characters can learn all classes, some characters will never be any good at certain roles), characters still retain their uniqueness. In X, Auron will always be the big hitter, like Fang is in XIII. Lulu and Yuna will always be the magic users, just like Hope and Vanille were in XIII.